Search Results (10)

This retrospective begins with Galvani’s experiments on frogs at the end of the 18th century and his discovery of ‘animal electricity’. It goes on to illustrate the numerous contributions to the field of physical chemistry in the second half of the 19th century (Nernst’s equilibrium potential, based on the work of Wilhelm Ostwald, Max Planck’s ion electrodiffusion, Einstein’s studies of Brownian motion) which led Bernstein to propose his membrane theory in the early 1900s as an explanation of Galvani’s findings and cell excitability. These processes were fully elucidated by Hodgkin and Huxley in 1952 who detailed the ionic basis of resting and action potentials, but without addressing the question of where these ions passed. The emerging question of the existence of ion channels, widely debated over the next two decades, was finally accepted and, a decade later, many of them began to be cloned. This led to the possibility of modelling the activity of individual neurons in the brain and then that of simple circuits. Taking advantage of the remarkable advances in computer science in the new millennium, together with a much deeper understanding of brain architecture, more ambitious scientific goals were dreamed of to understand the brain and how it works. The retrospective concludes by reviewing the main efforts in this direction, namely the construction of a digital brain, an in silico copy of the brain that would run on supercomputers and behave just like a real brain. Full article

Synaptic transmission is the main process providing cross-connecting activity among neurons in the central nervous system (CNS). In the present study, the 3D mathematical model of a neuronal bouton with a cluster localization of glycine receptors (GlyRs) on the post-synaptic membrane was developed. The number and eventual position of the receptors are defined by the structural data of the GlyR-gephyrin complex. Furthermore, the forming of inhibitory post-synaptic potential (IPSP) and an electro-diffusion of chloride ions were evaluated by applying the boundary problems for a Poisson’s equation and a non-steady-state diffusion equation, respectively. It was shown that local changes in the chloride ion concentration near the post-synaptic membrane, mediated by GlyRs activation, can raise up to 80–110% from the initial level. The average value of the concentration increase was as high as 10% in a pike of activity under the full activation of GlyRs. The central spatial localization of GlyRs in the cluster had a considerable difference both in the chloride ion concentration changes (6%) and IPSP (17%) compared to the divided or rear localization. Thus, a spatial polymorphism of the post-synaptic density of GlyRs is important to form a physiological response to a neuromediator release. Full article

Geochemistry and reactive transport play a critical role in many fields. In particular, calcite dissolution and precipitation are chemical processes occurring ubiquitously in the Earth’s subsurface. Therefore, understanding and quantifying them are necessary for various applications (e.g., water resources, reservoirs, geo-engineering). These fundamental geochemical processes can be monitored using the self-potential (SP) method, which is sensitive to pore space changes, water mineralization, and mineral–solution interactions. However, there is a lack of physics-based models linking geochemical processes to the SP response. Thus, in this study, we develop the first geochemical–geophysical fully coupled multi-species numerical workflow to predict the SP electrochemical response. This workflow is based on reactive transport simulation and the computation of a new expression for the electro-diffusive coupling for multiple ionic species. We apply this workflow to calcite dissolution and precipitation experiments, performed for this study and focused on SP monitoring alternating with sample electrical conductivity (EC) measurements. We carried out this experimental part on a column packed with calcite grains, equipped for multichannel SP and EC monitoring and subjected to alternating dissolution or precipitation conditions. From this combined experimental investigation and numerical analysis, the SP method shows clear responses related to ionic concentration gradients, well reproduced with electro-diffusive simulation, and no measurable electrokinetic coupling. This novel coupled approach allows us to determine and predict the location of the reactive zone. The workflow developed for this study opens new perspectives for SP applications to characterize biogeochemical processes in reactive porous media. Full article

In multispecies electrolyte solutions, each individual species can migrate according to its specific ionic properties. This process is called electrochemical migration or electro-diffusion and is well-described by the Nernst–Planck equation. The common approach for solving the corresponding mathematical system is based on the null current (NC) assumption, which expresses the electric potential in terms of charges and concentrations of chemical components. This assumption has a great advantage as it eliminates the electric potential from the Nernst–Planck equation. However, the NC assumption has limited capacities in describing electro-diffusion processes when the domain is subjected to an external electric field. The validity of the NC assumption could be questionable, even in the absence of an external electric field. This topic has never been investigated in the past. The main goal of this work is to evaluate the validity of the NC assumption and to understand its effect on the model outputs. Thus, we present a new reactive transport model that allows for a reliable representation of the electrochemical migration process. This model is based on the Nernst–Planck and Poisson (NPP) equations which are solved together. We also implement a model based on the NC assumption. Both models have been validated by comparison with CrunchFlow, based on several benchmarks. The results show that in the case of high sorptivity, the NC assumption is no longer valid. Therefore, in the case of sorption processes, the NPP should be used to simulate coulombic interactions. Full article

In the last few years, some advances have been made in the theoretical modelling of ion exchange processes in glass. On the one hand, the equations that describe the evolution of the cation concentration were rewritten in a more rigorous manner. This was made into two theoretical frameworks. In the first one, the self-diffusion coefficients were assumed to be constant, whereas, in the second one, a more realistic cation behaviour was considered by taking into account the so-called mixed ion effect. Along with these equations, the boundary conditions for the usual ion exchange processes from molten salts, silver and copper films and metallic cathodes were accordingly established. On the other hand, the modelling of some ion exchange processes that have attracted a great deal of attention in recent years, including glass poling, electro-diffusion of multivalent metals and the formation/dissolution of silver nanoparticles, has been addressed. In such processes, the usual approximations that are made in ion exchange modelling are not always valid. An overview of the progress made and the remaining challenges in the modelling of these unique processes is provided at the end of this review. Full article

We use stochastic simulations to investigate the performance of two recently developed methods for calculating the free energy profiles of ion channels and their electrophysiological properties, such as current–voltage dependence and reversal potential, from molecular dynamics simulations at a single applied voltage. These methods require neither knowledge of the diffusivity nor simulations at multiple voltages, which greatly reduces the computational effort required to probe the electrophysiological properties of ion channels. They can be used to determine the free energy profiles from either forward or backward one-sided properties of ions in the channel, such as ion fluxes, density profiles, committor probabilities, or from their two-sided combination. By generating large sets of stochastic trajectories, which are individually designed to mimic the molecular dynamics crossing statistics of models of channels of trichotoxin, p7 from hepatitis C and a bacterial homolog of the pentameric ligand-gated ion channel, GLIC, we find that the free energy profiles obtained from stochastic simulations corresponding to molecular dynamics simulations of even a modest length are burdened with statistical errors of only 0.3 kcal/mol. Even with many crossing events, applying two-sided formulas substantially reduces statistical errors compared to one-sided formulas. With a properly chosen reference voltage, the current–voltage curves can be reproduced with good accuracy from simulations at a single voltage in a range extending for over 200 mV. If possible, the reference voltages should be chosen not simply to drive a large current in one direction, but to observe crossing events in both directions. Full article

This work is aimed to give an electrochemical insight into the ionic transport phenomena in the cellular environment of organized brain tissue. The Nernst–Planck–Poisson (NPP) model is presented, and its applications in the description of electrodiffusion phenomena relevant in nanoscale neurophysiology are reviewed. These phenomena include: the signal propagation in neurons, the liquid junction potential in extracellular space, electrochemical transport in ion channels, the electrical potential distortions invisible to patch-clamp technique, and calcium transport through mitochondrial membrane. The limitations, as well as the extensions of the NPP model that allow us to overcome these limitations, are also discussed. Full article

Gastric mucus gel is known to exhibit dramatic and unique swelling behaviors in response to the ionic composition of the hydrating solution. This swelling behavior is important in the maintenance of the mucus layer lining the stomach wall, as the layer is constantly digested by enzymes in the lumen, and must be replenished by new mucus that swells as it is secreted from the gastric wall. One hypothesis suggests that the condensed state of mucus at secretion is maintained by transient bonds with calcium that form crosslinks. These crosslinks are lost as monovalent cations from the environment displace divalent crosslinkers, leading to a dramatic change in the energy of the gel and inducing the swelling behavior. Previous modeling work has characterized the equilibrium behavior of polyelectrolyte gels that respond to calcium crosslinking. Here, we present an investigation of the dynamic swelling behavior of a polyelectrolytic gel model of mucus. In particular, we quantified the rate at which a globule of initially crosslinked gel swells when exposed to an ionic bath. The dependence of this swelling rate on several parameters was characterized. We observed that swelling rate has a non-monotone dependence on the molarity of the bath solution, with moderate concentrations of available sodium inducing the fastest swelling. Full article

Living systems display a variety of situations in which non-equilibrium fluctuations couple to certain protein functions yielding astonishing results. Here we study the bacterial channel OmpF under conditions similar to those met in vivo, where acidic resistance mechanisms are known to yield oscillations in the electric potential across the cell membrane. We use a three-dimensional structure-based theoretical approach to assess the possibility of obtaining fluctuation-driven transport. Our calculations show that remarkably high voltages would be necessary to observe the actual transport of ions against their concentration gradient. The reasons behind this are the mild selectivity of this bacterial pore and the relatively low efficiencies of the oscillating signals characteristic of membrane cells (random telegraph noise and thermal noise). Full article

Antimicrobial peptides (AMPs) are naturally-occurring molecules that exhibit strong antibiotic properties against numerous infectious bacterial strains. Because of their unique mechanism of action, they have been touted as a potential source for novel antibiotic drugs. We present a summary of computational investigations in our lab aimed at understanding this unique mechanism of action, in particular the development of models that provide a quantitative connection between molecular-level biophysical phenomena and relevant biological effects. Our work is focused on protegrins, a potent class of AMPs that attack bacteria by associating with the bacterial membrane and forming transmembrane pores that facilitate the unrestricted transport of ions. Using fully atomistic molecular dynamics simulations, we have computed the thermodynamics of peptide-membrane association and insertion, as well as peptide aggregation. We also present a multi-scale analysis of the ion transport properties of protegrin pores, ranging from atomistic molecular dynamics simulations to mesoscale continuum models of single-pore electrodiffusion to models of transient ion transport from bacterial cells. Overall, this work provides a quantitative mechanistic description of the mechanism of action of protegrin antimicrobial peptides across multiple length and time scales. Full article